Rural-Urban Disparities in Five Leading Causes of Mortality in the United States

An Overview of the Data

This interactive plot examines the differences of Standardized Mortality Ratio (SMR), the proportion between observed death and expected death, of the five causes of death in each public health region. Each observation indicates for which state it belongs to with the size of which is reflective of the corresponding population. Here we compare SMR within the same geographic area. The differences of the distribution of the SMR among five causes of deaths might associate with the sociodemographic, cultural, behavioral and structural factors of the specific region.

cod_data %>%
  mutate(year = as.factor(year))
## # A tibble: 191,748 x 12
##      year age_range cause_of_death   state        locality observed_deaths
##    <fctr>     <chr>          <chr>   <chr>           <chr>           <int>
##  1   2005      0-49         Cancer Alabama             All             756
##  2   2005      0-49         Cancer Alabama    Metropolitan             556
##  3   2005      0-49         Cancer Alabama Nonmetropolitan             200
##  4   2005      0-49         Cancer Alabama             All             756
##  5   2005      0-49         Cancer Alabama    Metropolitan             556
##  6   2005      0-49         Cancer Alabama Nonmetropolitan             200
##  7   2005      0-49         Cancer Alabama             All             756
##  8   2005      0-49         Cancer Alabama    Metropolitan             556
##  9   2005      0-49         Cancer Alabama Nonmetropolitan             200
## 10   2005      0-54         Cancer Alabama             All            1346
## # ... with 191,738 more rows, and 6 more variables: population <int>,
## #   expected_deaths <int>, potentially_excess_deaths <int>,
## #   percent_excess_death <dbl>, mortality <dbl>, hhs_region <int>
p <- cod_data %>%
  plot_ly(
    x = ~expected_deaths, 
    y = ~observed_deaths, 
    size = ~population, 
    color = ~cause_of_death, 
    frame = ~hhs_region, 
    text = ~state, 
    hoverinfo = "text",
    type = 'scatter',
    mode = 'markers'
  ) %>% 
  layout(title = "Change of Standardized Mortality Ratio in National Public Health Regions", yaxis=list(title="Observed Death"),xaxis=list(title="Expected Death"))

p

Here we show the division of the 10 U.S. Department of Health and Human Services public health regions in the figure below.

From the linear regression plot below, we can see that the mortality of cancer, unintentional injury in both metropolitan regions and nonmetropolitan regions decrease through years 2005-2015. In contrast, the mortality of heart disease and chronic lower respiratory disease in both metropolitan regions and nonmetropolitan regions increase through years 2005-2015. For stroke, the mortality in metropolitan regions decreases through years 2005-2015 whereas the mortality in metropolitan regions slightly increases through years 2005-2015. Concerning mortality and the trend in mortality, unintentional injury and heart disease needs more attention from public health experts.

Descriptive Analysis

Mortality for five leading causes of death by locality

#mortality~year+cause
cod_datayr2 = read_csv("./data/NCHS_-_Potentially_Excess_Deaths_from_the_Five_Leading_Causes_of_Death.csv") %>%
  clean_names() %>%
  na.omit() %>%
  filter(!(state == "United States")) %>%
  separate(., percent_potentially_excess_deaths, into = c("percent_excess_death"), sep = "%") %>%
  mutate(percent_excess_death = as.numeric(percent_excess_death), mortality = observed_deaths/population * 10000, mortality = as.numeric(mortality)) %>%
  select(year, cause_of_death, state, benchmark, locality, observed_deaths, population, expected_deaths, potentially_excess_deaths, percent_excess_death, mortality)
## Parsed with column specification:
## cols(
##   Year = col_integer(),
##   `Cause of Death` = col_character(),
##   State = col_character(),
##   `State FIPS Code` = col_character(),
##   `HHS Region` = col_integer(),
##   `Age Range` = col_character(),
##   Benchmark = col_character(),
##   Locality = col_character(),
##   `Observed Deaths` = col_integer(),
##   Population = col_integer(),
##   `Expected Deaths` = col_integer(),
##   `Potentially Excess Deaths` = col_integer(),
##   `Percent Potentially Excess Deaths` = col_character()
## )
## Warning: Too many values at 191748 locations: 1, 2, 3, 4, 5, 6, 7, 8, 9,
## 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...

lineplotyr = cod_datayr2 %>%
  filter(benchmark == "2010 Fixed",
         locality == c("Metropolitan", "Nonmetropolitan"))%>%
  group_by(cause_of_death,year, locality)%>%
  distinct(year, cause_of_death, locality, .keep_all = TRUE)%>%
  ungroup(year, cause_of_death)%>%
  ggplot(aes(x = year, y = mortality, group = locality, color = locality))+
  geom_point(size = 0.5)+
  geom_smooth(method = lm, size = 0.5,se=FALSE) +
  facet_grid(.~cause_of_death)+
  theme(axis.text.x = element_text(angle = 45, hjust = 1))+
  labs(x = "") +
  scale_x_continuous( breaks=seq(2005,2015,1))
  ggplotly(lineplotyr) %>% 
  layout(
     #xaxis = list(showticklabels = FALSE),
     legend = list(orientation = "h",
<<<<<<< HEAD
                   y = -0.1, x = 0.3))

cod_data %>%
  mutate(cause_of_death = fct_reorder(cause_of_death, mortality)) %>% 
  group_by(cause_of_death) %>% 
  ggplot(aes(x = cause_of_death, y = mortality, color = cause_of_death)) +
  geom_boxplot() +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  labs(title="Locality vs. Mortality") +
  labs(x="Locality", y="Mortality", color = "Cause of Death") +
  facet_grid(~locality)

This bar graph shows the distribution of cause of death within mortality in the three geographic regions: Metropolitan, Nonmetropolitan and All. We observe that the rank in causes of death is the same regardless of the locality. Nonmetropolitan area seems to have the highest mortaility, the number of deathes observed in every 10000 people. We observe that the median of mortaility of Cancer is the highest among all 5 causes of death, followed by heart disease, unintentional injury, chronic lower respiratory disease and stroke. All 5 causes of death are right skewed regardless of the locality.

Linear Model

To further support our graphs above, linear regression is performed between mortality and locality. The result shows that metropolitan regions have on average less mortality compared with nonmetropolitan regions.

mortality_lm = lm(mortality ~locality, data = cod_data)
summary(mortality_lm)
## 
## Call:
## lm(formula = mortality ~ locality, data = cod_data)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -5.1454 -2.9547 -1.2983  0.9988 19.8959 
## 
## Coefficients:
##                         Estimate Std. Error t value Pr(>|t|)    
## (Intercept)              4.10331    0.01672 245.474   <2e-16 ***
## localityMetropolitan    -0.22576    0.02372  -9.519   <2e-16 ***
## localityNonmetropolitan  1.14451    0.02438  46.942   <2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 4.317 on 191745 degrees of freedom
## Multiple R-squared:  0.01821,    Adjusted R-squared:  0.0182 
## F-statistic:  1778 on 2 and 191745 DF,  p-value: < 2.2e-16
rl3 = broom::tidy(mortality_lm)
kable(rl3)

Data Visualization

Does mean percent excess death have significant difference between metro and non-metro groups?

gp_cod_data = cod_data %>%
  group_by(year, locality) %>% 
  summarise(mean_ped = mean(percent_excess_death)) 

gp_cod_data_Metro = gp_cod_data %>%
  group_by(year) %>%
  filter(locality == "Metropolitan")
gp_cod_data_nonMetro = gp_cod_data %>%
  group_by(year) %>%
  filter(locality == "Nonmetropolitan")
gp_cod = cbind(gp_cod_data_Metro, gp_cod_data_nonMetro)

p = gp_cod %>%
plot_ly( x = ~year, y = ~mean_ped, name = 'Metropolitan', type = 'scatter', mode = 'markers') %>%
  add_trace( y = ~mean_ped1, name = 'Nonmetropolitan', mode = 'markers') %>% 
  layout(yaxis = list(title = 'mean percent excess death (Metropolitan/Nonmetropolitan)'))
p

The above plot shows the gap of mean percent excess death for metropolitan and nonmetropolitan. Nonmetropolitan has a obviously larger mean percent excess death than metropolitan areas. In order to see if the difference is significant, we will run a regression analysis regarding mean excess death and locality.

Regression Analysis

The regression model is mean percent_excess_death = 33.89 - 2.05Metropolitan + 8.046Nonmetropolitan.
For people in metropolitan, the expected percent excess death has a decrease of 2.06. * For people in non-metropolitan area, the expected percent excess death has an increase of 8.046. * The p-values show these predictors are both significant. Therefore, we conclude that there is significant difference in mean percent excess death between Metropolitan and Nonmetropolitan Area.

gp_locality_lm = lm(mean_ped ~locality , data = gp_cod_data)
summary(gp_locality_lm)
## 
## Call:
## lm(formula = mean_ped ~ locality, data = gp_cod_data)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -1.5667 -1.0325 -0.3470  0.7922  3.2937 
## 
## Coefficients:
##                         Estimate Std. Error t value Pr(>|t|)    
## (Intercept)              33.8866     0.4071  83.238  < 2e-16 ***
## localityMetropolitan     -2.0599     0.5757  -3.578   0.0012 ** 
## localityNonmetropolitan   8.0460     0.5757  13.975 1.13e-14 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 1.35 on 30 degrees of freedom
## Multiple R-squared:  0.9198, Adjusted R-squared:  0.9145 
## F-statistic: 172.1 on 2 and 30 DF,  p-value: < 2.2e-16
rl4 = broom::tidy(gp_locality_lm)
kable(rl4)

Account for Year

How should we help nonmetropolitan areas improve public health?

cod_datayr2 = read_csv("./data/NCHS_-_Potentially_Excess_Deaths_from_the_Five_Leading_Causes_of_Death.csv") %>%
  clean_names() %>%
  na.omit() %>%
  filter(!(state == "United States")) %>%
  separate(., percent_potentially_excess_deaths, into = c("percent_excess_death"), sep = "%") %>%
  mutate(percent_excess_death = as.numeric(percent_excess_death), mortality = observed_deaths/population * 10000, mortality = as.numeric(mortality)) %>%
  select(year, cause_of_death, state, benchmark, locality, observed_deaths, population, expected_deaths, potentially_excess_deaths, percent_excess_death, mortality)
## Warning: Too many values at 191748 locations: 1, 2, 3, 4, 5, 6, 7, 8, 9,
## 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...

As can be seen in the following plot, if we stratify by cause of death, we will find some increasing pattern of mean percentage of excess death in subgroups(unintentional injury) and some decreasing patterns in other subgroups(cancer, heart disease, etc). In nonmetropolitan regions(right), unintentional injury and chronic lower respiratory disease have on average the highest excess death percentage in nonmetropolitan areas and need more attention from public health experts.

cod_datayr2 %>%
  filter(benchmark == "2010 Fixed") %>%
  group_by(cause_of_death,year, locality) %>%
  mutate(year_percent_death=mean(percent_excess_death)) %>%
  distinct(year, cause_of_death, locality, .keep_all = TRUE) %>%
  ungroup(year, locality) %>%
  ggplot(aes(x = year, y = year_percent_death, color = cause_of_death)) +
  geom_point(size = 1) +
  geom_line(size = 1) +
  facet_grid(.~locality) +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  scale_x_continuous( breaks=seq(2005,2015,1)) +
  labs(
    title = "Average yearly excess death percentage for different locality",
    color = "Cause of Death",
    y = "Yearly Mean percentage of Excess Death"
    )

cod_datayrlm = cod_datayr2 %>%
  filter(locality == "Nonmetropolitan",
         benchmark == "2010 Fixed")
lmpop = lm(data = cod_datayrlm, percent_excess_death ~ year+cause_of_death)
summary(lmpop)
## 
## Call:
## lm(formula = percent_excess_death ~ year + cause_of_death, data = cod_datayrlm)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -55.456  -9.828   0.576  10.404  39.489 
## 
## Coefficients:
##                                                  Estimate Std. Error
## (Intercept)                                     769.06335   67.48938
## year                                             -0.36941    0.03358
## cause_of_deathChronic Lower Respiratory Disease  27.06490    0.33901
## cause_of_deathHeart Disease                      13.90257    0.32844
## cause_of_deathStroke                             12.91441    0.33784
## cause_of_deathUnintentional Injury               31.18470    0.32812
##                                                 t value Pr(>|t|)    
## (Intercept)                                       11.39   <2e-16 ***
## year                                             -11.00   <2e-16 ***
## cause_of_deathChronic Lower Respiratory Disease   79.83   <2e-16 ***
## cause_of_deathHeart Disease                       42.33   <2e-16 ***
## cause_of_deathStroke                              38.23   <2e-16 ***
## cause_of_deathUnintentional Injury                95.04   <2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 14.92 on 19718 degrees of freedom
## Multiple R-squared:  0.365,  Adjusted R-squared:  0.3649 
## F-statistic:  2267 on 5 and 19718 DF,  p-value: < 2.2e-16
rl5 = broom::tidy(lmpop)
kable(rl5)

Account for Locality

For each of the five cause of death, what is the mean percent of excess death? It is different across locality.

As shown in the boxplots for all three regions, the rank of mean percentage of excess death of the five cause of death remain the same for different localities. For all five causes, the mean percent of death is lower for Metropolitan than Nonmetropolitan.

cod_data %>%
  select(state, locality, percent_excess_death, hhs_region, cause_of_death) %>%
  filter(locality != "All") %>% 
  mutate(hhs_region = as.factor(hhs_region)) %>% 
  group_by(cause_of_death, locality) %>% 
  summarise(mean_ped = mean(percent_excess_death)) %>% 
  ungroup() %>% 
  ggplot(aes(x = cause_of_death,  y = mean_ped, fill = cause_of_death)) +
  geom_col() +
  facet_grid(~locality) +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  labs(
    x = "Five Leading Causes of Death",
    y = "Mean Percentage of Excess Death",
    fill = "Causes of Death"
  )

Account for HHS Regions

#Mean percent excess deaths ~ hhs_region
region_lm = lm(region_cod_data$mean_ped~region_cod_data$hhs_region)
rl1 = broom::tidy(region_lm)
kable(rl1)

#Mean percent excess deaths ~ hhs_region + locality
region_locality_lm = lm(region_cod_data$mean_ped ~ region_cod_data$hhs_region+region_cod_data$locality)
rl2 = broom::tidy(region_locality_lm)
kable(rl2)

cod_data %>%
  select(state, locality, percent_excess_death, hhs_region, cause_of_death) %>%
  filter(locality != "All") %>% 
  group_by(cause_of_death, locality, hhs_region) %>% 
  summarise(mean_ped = mean(percent_excess_death)) %>% 
  mutate(hhs_region = as.factor(hhs_region)) %>% 
  ggplot(aes(x = hhs_region,  y = mean_ped, fill = hhs_region)) +
  geom_col() +
  facet_grid(~cause_of_death) +
  theme(axis.text.x = element_text(angle = 15)) +
    labs(
      y = "Mean %Excess Death",
      x = "HHS Regions",
      fill = "HHS Region"
    ) 

map_cod_data = cod_data %>%
  filter(locality == "Metropolitan") %>%
  select(state, locality, percent_excess_death) %>% 
  group_by(state) %>% 
  summarise(mean_ped = mean(percent_excess_death)) %>% 
  dplyr::filter(!(state == "District of\nColumbia"))
  

map = as.tibble(fifty_states) %>%
  group_by(id) %>% 
  summarize(clong = mean(long), clat = mean(lat)) %>% 
  filter(!(id == "district of columbia"))

df <- cbind(map, state.abb, state.center, rate = unique(map_cod_data$mean_ped))

ggplot(df, aes(map_id = id)) + 
    geom_map(aes(fill = rate), map = fifty_states) + 
    expand_limits(x = fifty_states$long, y = fifty_states$lat) + 
    labs(x = "", y = "") +
    theme(panel.background = element_blank(), 
          axis.text.x = element_blank(), 
          axis.text.y = element_blank(), 
          axis.ticks = element_blank()) + 
    geom_text(aes(x = clong, y = clat, label = state.abb)) +
  scale_fill_gradient(low="gold", high="red")